From mlorenz@ecn.purdue.edu Tue May 18 18:58:34 1993 Date: Tue, 18 May 93 23:58:34 -0500 From: mlorenz@ecn.purdue.edu (Michael Lorenz) Message-Id: <9305190458.AA23114@cn.ecn.purdue.edu> To: CHEMISTRY@ccl.net Subject: Gaussian-density matrix problem Dear Netters, I'm sort of new to ab initio calculations (specifically Gaussian90)& I've been trying to optimize dimethyl ether just to get a feel for the program and I've been running into a symmetry problem. More precisely, the program is giving me a symmetry error in the PCHEK subroutine. I've been using a mimimal basis set and 6-31g*(in case the exclusion of the polarization functions might of had something to do with my problem). Could anyone offer suggestions to why this is happening? I'd greatly appreciate any help. Thanks, Mike Lorenz Graduate Student Purdue University From topper@haydn.chm.uri.edu Wed May 19 08:10:47 1993 Date: Wed, 19 May 93 12:10:47 -0400 From: topper@haydn.chm.uri.edu (Robert Q. Topper) Message-Id: <9305191610.AA04675@haydn.chm.uri.edu> To: CHEMISTRY@ccl.net Subject: high-order moments Dear netters; I have the need to compute electrostatic moments (quadrupole, octupole, etc., etc. ...) for molecules, given their equilibrium geometries and point charges defined for each atom. Before I re-create the wheel, does anyone know of publicly available (shareware/freeware) software which will do this? I'm running on an Iris Indigo 4000. Many thanks, Robert ******************************** * Dr. Robert Q. Topper, PRA * * Department of Chemistry * * University of Rhode Island * * Kingston, RI 02881 USA * ******************************** * topper@haydn.chm.uri.edu * * (401) 792-2597 [office] * * (401) 792-5072 [FAX] * ******************************** "...what is truth?" -Johnny Cash From schurko@ccu.UManitoba.CA Wed May 19 07:30:34 1993 Date: Wed, 19 May 1993 12:30:34 -0500 (CDT) From: Robert Schurko Subject: Re: Gaussian-density matrix problem To: Michael Lorenz Message-Id: On Tue, 18 May 1993, Michael Lorenz wrote: > > Dear Netters, > > I'm sort of new to ab initio calculations (specifically Gaussian90)& I've > been trying to optimize dimethyl ether just to get a feel for the program and > I've been running into a symmetry problem. More precisely, the program is > giving me a symmetry error in the PCHEK subroutine. I've been using > a mimimal basis set and 6-31g*(in case the exclusion of the polarization > functions might of had something to do with my problem). Could anyone offer > suggestions to why this is happening? I'd greatly appreciate any help. > > Thanks, > > Mike Lorenz > Graduate Student > Purdue University > > --- > Administrivia: This message is automatically appended by the mail exploder: > CHEMISTRY@ccl.net --- everyone CHEMISTRY-REQUEST@ccl.net --- coordinator > OSCPOST@ccl.net send help from chemistry Anon. ftp www.ccl.net > CHEMISTRY-SEARCH@ccl.net --- search the archives, read help.search file first > --- > Why don't you initially try a lower basis to begin with, such as an STO-3G basis set. Commonly, when higher basis sets, such as a 6-31g* are desired, one must "work up" to that level by starting out with something a little more elementary. Secondly, how are you constructing the molecule? If you are using a z-matrix, and you are running into symmetry problems, you might be simply specifying some element as symmetry exchangeable, when it actually isn't. If you are using a graphical method, or simply cartesian coordinates, I would first consider a low level semi-empirical calculation to get proper geometries, etc. Hope this helps, Rob ============================================================================= schurko@ccu.umanitoba.ca Robert Schurko Chemistry Department (204)-474-9335 University of Manitoba Winnipeg, MB, CANADA ============================================================================= From jas@medinah.atc.ucarb.com Wed May 19 12:01:03 1993 Message-Id: <9305192102.AA14866@medinah.atc.ucarb.com> Date: Wed, 19 May 1993 17:01:03 -0500 To: chemistry@ccl.net From: jas@medinah.atc.ucarb.com (Jack Smith) Subject: Re: 3D to 2D ball and stick models >I have alot of MacroModel molecule files which I would like to >display in memos and journal articles. For those places that color >CPK displays are appropriate, a screen image is fine. However, >for black and white photocopies and many memos, a 'ORTEP-like", or >"ball and stick" representation with hidden line removal would be best. > >Does anybody have suggestions for how to do this with PC software, >or Unix software, preferably resulting in postscript output? > I find MSC XMol's output quite sufficient. CAChe's "Schematic" print option is also quite good. There are also various ORTEP programs (like NAMOD from QCPE) floating around. -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JACK A. SMITH ...................................................................... Union Carbide Corp. || Phone: (304) 747-5797 Catalyst Skill Center || FAX: (304) 747-5571 P.O. Box 8361 || S. Charleston, WV 25303 || Internet: jas@medinah.atc.ucarb.com -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From mlorenz@ecn.purdue.edu Wed May 19 10:56:14 1993 Date: Wed, 19 May 93 15:56:14 -0500 From: mlorenz@ecn.purdue.edu (Michael Lorenz) Message-Id: <9305192056.AA29648@cn.ecn.purdue.edu> To: CHEMISTRY@ccl.net Subject: Gaussian-density matrix problem Dear Netters, I would like to thank everyone for responding to my message--this is very encouraging; A few asked that I send my input file so that they could take a look at and see where I messed up. So here it is: # HF/STO-3G OPT DIMETHYL ETHER STO-3G STRUCTURE UNCONSTRAINED 0 1 O C 1 RCO1 H 2 RCH1 1 HCO1 H 2 RCH2 1 HCO2 3 HCH1 H 2 RCH3 1 HCO3 3 HCH2 C 1 RCO2 2 COC 3 HCOC1 H 6 RCH4 1 HCO4 2 HCOC2 H 6 RCH5 1 HCO5 7 HCH3 H 6 RCH6 1 HCO6 7 HCH4 RCH1 1.09 RCH2 1.09 RCH3 1.09 RCH4 1.09 RCH5 1.09 RCH6 1.09 RCO1 1.40 RCO2 1.40 HCO1 109.5 HCO2 109.5 HCO3 109.5 HCO4 109.5 HCO5 109.5 HCO6 109.5 COC 109.5 HCH1 120. HCH2 -120. HCH3 120. HCH4 -120. HCOC1 180. HCOC2 180. Again, I appreciate everyone taking the time to help me. Mike Lorenz Purdue Graduate Student From topper@haydn.chm.uri.edu Wed May 19 14:07:34 1993 Date: Wed, 19 May 93 18:07:34 -0400 From: topper@haydn.chm.uri.edu (Robert Q. Topper) Message-Id: <9305192207.AA05651@haydn.chm.uri.edu> To: chemistry@ccl.net, topper@haydn.chm.uri.edu Subject: Re: high-order moments Hello again, sorry to waste bandwidth but based on several early responses to my previous query I was not sufficiently clear in what I am looking for. > > Dear netters; > > I have the need to compute electrostatic moments (quadrupole, octupole, > etc., etc. ...) for molecules, given their equilibrium geometries and > point charges defined for each atom. > > Before I re-create the wheel, does anyone know of publicly available > (shareware/freeware) software which will do this? I am not doing ab initio work on molecules, extracting point charges, and then trying to calculate multipoles. Rather, I am interested in evaluating some of the point-charge models which are commonly used in liquid simulation work. So, for example, I'd like to be able to calculate the octupole-octupole contribution to the interaction energy of two rigid molecules as a function of their relative orientation and distance apart. Apparently there has been some excellent work done on calculating multipole moments from ab initio wave functions, but this work isn't helpful to me. I need multipole moments extracted from point charge models. Thanks again to all (including those who have already written!). I'll summarize what I find to the net. best, robert ******************************** * Dr. Robert Q. Topper, PRA * * Department of Chemistry * * University of Rhode Island * * Kingston, RI 02881 USA * ******************************** * topper@haydn.chm.uri.edu * * (401) 792-2597 [office] * * (401) 792-5072 [FAX] * ******************************** "...what is truth?" -Johnny Cash From soperpd@esvax.dnet.dupont.com Wed May 19 15:56:42 1993 Date: Wed, 19 May 93 19:56:42 -0400 Message-Id: <9305192356.AA03041@esds01.es.dupont.com> From: soperpd@esvax.dnet.dupont.com To: "chemistry@ccl.net"@esds01.dnet.dupont.com Subject: Cheap Comp Chem Clarification I have disturbed some of my colleagues at DuPont (and others) with my earlier posting asking about 'Computational Chemistry on the Cheap.' For the record, DuPont has excellent facilities for computational chemistry (including a Cray) and equally good people supporting them. The question was inspired by observing the difficulty of doing scientific research at universities in the 'third world.' Someone from, say, Kenya who earns a Ph.D. in chemistry (almost always in the U.S. or Europe) is faced with the choice of either going home and giving up virtually all research, or continuing their research but remaining an expatriate. Might computational chemistry be a field which this Kenyan could teach at the University of Nairobi without losing all ability to do research? My apologies for implying that the question referred to DuPont's computational chemistry environment. When posting the original question I didn't think my motivation was worth the bandwidth, but I stand corrected. Paul Soper soperpd@esvax.dnet.dupont.com From dave@carbon.chem.csiro.au Thu May 20 08:10:19 1993 Message-Id: <199305200310.AA01883@shark.mel.dit.csiro.au> Date: Thu, 20 May 93 13:10:19 EST From: (Dr.) Dave Winkler Subject: Structure display from SMILES To: chminf-l@iubvm.ucs.indiana.edu, chemistry@ccl.net I need a program which runs on a Mac (or PC if there is no other choice) which can read a SMILES string and draw a 2-D or 3-D structure. The MedChem software will do this and much more but it doesnt run on a Mac. As far as I can see ChemDraw, Chem3D, MacMolecule etc cannot do it (although ChemDraw can do the reverse!). Can anyone help? Cheers, Dave __________________________________________________________________________ Dr. David A. Winkler Voice: 61-3-542-2244 Principal Research Scientist Fax: 61-3-543-8160 CSIRO Division of Chemicals and Polymers Private Bag 10 Clayton, Australia. "Life is what happens to you while you're making other plans"